[R-pkg-devel] Two errors

[Jiří Moravec]

I would like to add that copy pasting is also a valid way to include 
dependencies.

Just make sure to get contributions right.

-- Jirka

On 5/07/25 11:19, Michael Chirico wrote:
> Sharon, Luke noted that (somewhat strangely [1]) {ape} is exporting the
> registered entry point for that routine, so you should just be able to do:
>
> importFrom(ape,seq_root2tip)
>
> and be on your way.
>
> [1] ?ape::seq_root2tip notes that "other packages" use it, but none of
> those are on CRAN, could be a Bioconductor thing:
> https://github.com/search?q=org%3Acran+%2Fseq_root2tip%5Cb%2F+lang%3AR+-repo%3Acran%2Fape&type=code
>
> Mike C
>
> On Fri, Jul 4, 2025 at 4:03 PM Sharon Bewick <sbewick using clemson.edu> wrote:
>
>> So I think the only solution that CRAN will accept is linking against
>> headers. I can download an ape.h header file, but for the life of me, I’m
>> having trouble figuring out how to link it in my R package. I’ve read what
>> I can find online, but haven’t been successful. Right now, I have the ape.h
>> file in an src folder. I also have
>>
>> LinkingTo: Rcpp, ape
>>
>> In my DESCRIPTION file
>>
>>
>>
>> But I’m getting all sorts of errors. Does anyone have an example of how I
>> can do this that I might be able to work from?
>>
>>
>>
>> Thanks in advance!!!!
>>
>> Sharon
>>
>>
>>
>>
>>
>> *From: *Iris Simmons <ikwsimmo using gmail.com>
>> *Date: *Thursday, July 3, 2025 at 5:11 PM
>> *To: *Sharon Bewick <sbewick using clemson.edu>
>> *Cc: *Michael Chirico <michaelchirico4 using gmail.com>, R Package Development <
>> r-package-devel using r-project.org>
>> *Subject: *Re: [R-pkg-devel] Two errors
>>
>> This Message Is From An External Sender: Use caution when opening links or
>> attachments if you do not recognize the sender.
>>
>> I believe the suggestion was that you should alternatively write:
>>
>> .Call("seq_root2tip", nt$edge, length(nt$tip.label), nt$Nnode, PACKAGE =
>> "ape")
>>
>> however, that generates the following note that CRAN is very unlikely to
>> accept:
>>
>> * checking foreign function calls ... NOTE
>> Foreign function call to a different package:
>>    .Call("seq_root2tip", ..., PACKAGE = "ape")
>> See chapter 'System and foreign language interfaces' in the 'Writing R
>> Extensions' manual.
>>
>> The other possibility is adding:
>>
>> importFrom(ape, seq_root2tip)
>>
>> to your NAMESPACE and not modifying your code, but that generates a
>> different note:
>>
>> * checking foreign function calls ... NOTE
>> Registration problem:
>>    symbol 'seq_root2tip' not in namespace:
>>     .Call(seq_root2tip, ...)
>> See chapter 'System and foreign language interfaces' in the 'Writing R
>> Extensions' manual.
>>
>> Your best bet is to ask the maintainers of package:ape to add and
>> export an R function like this:
>>
>> idk <- function (...)
>> .Call(seq_root2tip, ...)
>>
>> There are also ways to do it in C using R_RegisterCCallable and
>> R_GetCCallable but that might be too complicated for something like
>> this.
>>
>> On Thu, Jul 3, 2025 at 6:33 PM Sharon Bewick <sbewick using clemson.edu> wrote:
>>> Thanks so much for the tips!
>>>
>>> I think I’ve fixed #2. But I’m not sure what you mean by #1. Where
>> should the "seq_root2tip" with PACKAGE="ape" go? In the NAMESPACE file? In
>> the Description file? Somewhere in the code?
>>> So sorry for not understanding!
>>>
>>> Thanks!
>>> Sharon
>>>
>>> From: Michael Chirico <michaelchirico4 using gmail.com>
>>> Date: Thursday, July 3, 2025 at 4:13 PM
>>> To: Sharon Bewick <sbewick using clemson.edu>
>>> Cc: R Package Development <r-package-devel using r-project.org>
>>> Subject: Re: [R-pkg-devel] Two errors
>>>
>>> This Message Is From An External Sender: Use caution when opening links
>> or attachments if you do not recognize the sender.
>>> 1. all functions in R are variables. You can "trick" code tools by
>> writing seq_root2tip=NULL in the same scope but consider (a) C routines are
>> typically part of a package's private interface (b) it might be preferable
>> to use the string "seq_root2tip" with PACKAGE="ape"
>>> 2. phytree is not the same as phytree<- : importFrom(phyloseq,
>> "phytree<-") is what you want assuming it's exported)
>>> (c.f. `x = phyteee(...)` vs. `phytree(x) <- ...`)
>>>
>>> Mike C
>>> On Thu, Jul 3, 2025, 2:57 PM Sharon Bewick <sbewick using clemson.edu<mailto:
>> sbewick using clemson.edu>> wrote:
>>> 1. I’m trying to upload my R package. However, I use the ape function
>> seq_root2tip but for the sake of speed am calling it using .Call:
>>> toroot<-.Call(seq_root2tip, nt$edge, length(nt$tip.label), nt$Nnode)
>>>
>>> How do I get R to recognize the seq_root2tip function from ape in this C
>> call? It is throwing up a NOTE that is getting my package rejected:
>>> shade_branch: no visible binding for global variable ‘seq_root2tip’
>>>
>>> but seq_root2tip is a function, not a global variable.
>>>
>>> 2. I’m also getting a NOTE about: no visible global function definition
>> for ‘phy_tree<-’
>>> I have declared phy_tree in the NAMESPACE file:
>> importFrom(phyloseq,phy_tree)
>>> I don’t know what the problem is…
>>>
>>> Thanks!
>>> Sharon
>>>
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>>>
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